I've been working on a mod for a while using unity 4, I've noticed that the fix I found for some rendering issues (Changing TileManagerScript's initialization to start rather than awake) only fixes things as long as your window remains static and unmoved, this issue isn't present in builds using 3.5.6 as far as I'm aware but another and I presume connected bug in that alt-tabbing while fullscreen corrupts all tiles is.

If anyone has an idea of how to fix these issues I'd very much appreciate the help on sorting it.

These seem to be effects of trying to build the game with the free version of unity. The garbled graphics are rendered using a pro-only feature called render to texture. It's curious how you were able to fix some of the problems though, but I think that might've been some fluke rather than a fix unless you're using unity pro.